The Nondeterministic Waiting Time Algorithm: A Review

TL;DR

The paper reviews the Nondeterministic Waiting Time algorithm, a versatile method for simulating biochemical networks that can replicate Gillespie's stochastic approach or deterministic ODE solutions based on system parameters.

Contribution

It provides a comprehensive description of the algorithm, its implementation details, and demonstrates its application to biologically relevant models.

Findings

Successfully mimicked Gillespie Algorithm for certain networks.

Produced ODE-like solutions for other networks.

Applied to Fas-mediated apoptosis in cancer and HIV-infected T cells.

Abstract

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells.